Convert Blast output to tabular

[Rsola]

Hi,

Does anybody know how to convert Blast Output as below to a tabular (.csv) output or how to extract top hits? In the online tool that I use I can't select for tabular output.

Thanks!

Query= OsSNP0002
(142 letters)

Database: ../uniprot-oryza-sativa-indica.fasta
42,240 sequences; 15,872,719 total letters

Searching..................................................done



Score E
Sequences producing significant alignments: (bits) Value

tr|A2WJN5|A2WJN5_ORYSI Putative uncharacterized protein OS=Oryza... 55 2e-18
tr|B8AKP7|B8AKP7_ORYSI Putative uncharacterized protein OS=Oryza... 53 6e-17
tr|B8AEL6|B8AEL6_ORYSI Putative uncharacterized protein OS=Oryza... 28 1.5
tr|B8B114|B8B114_ORYSI Putative uncharacterized protein OS=Oryza... 28 2.0
tr|B8AQS5|B8AQS5_ORYSI Putative uncharacterized protein OS=Oryza... 27 2.6
tr|B8ADP7|B8ADP7_ORYSI Putative uncharacterized protein OS=Oryza... 27 4.4
tr|A2ZKU4|A2ZKU4_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5
tr|A2Y774|A2Y774_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5
tr|A2WXP8|A2WXP8_ORYSI Putative uncharacterized protein OS=Oryza... 25 9.7 [/SIZE][/SIZE]

[lran2008]

You could choose the Blast output format by setting -outfmt. Try -outfmt 6 .

[Rsola]

Thank you for your reply, but like I indicated, I can't set the output format in the online tool that I used (no command lines in the tool). This is the output I have to deal with.

[lran2008]

Thank you for your reply, but like I indicated, I can't set the output format in the online tool that I used (no command lines in the tool). This is the output I have to deal with.

Sorry, I didn't notice it. I don't know what's the output format by online blast. But if it can be opened by excel or be imported in to R, you could get what you want then.

[GenoMax]

Are you able to use the command line/have access to python? Following may work in that case

https://bitbucket.org/ctb/ngs-course/src/14e27b32946f0341f3abdcff6d6c7536186a3205/blast/parse-blast-to-csv.py?at=default

Extended in this post:

http://haotu.wordpress.com/2012/03/07/parse-filter-blast-output-to-csv-excel/

[rhinoceros]

I'm not really following how your output is formatted, but I'm sure clever use of e.g. sed could solve your problem. That or using blast_formatter (if your output is asn.1)..

[GenoMax]

If you used NCBI to do the search then you can download the results as "hit table.csv" file under the "download" option on the results page.

[SDPA_Pet]

Hi GenoMax,

Actually, it is more complicated. The blast output was extracted from MEGAN. It was originally blasted using -m 0 format. I extracted some blast output of some pathways in order to look at the details. I would like to report the highest hit score species in my paper. So, it would be easy for me to convert it to tabular format.